Epigenetic mechanisms, including DNA methylation, play crucial roles in regulating gene expression, influencing phenotypic variation, and facilitating responses to environmental pressures. Bisulfite sequencing has long been the gold standard for studying DNA methylation in ecological and evolutionary contexts. However, this method has significant limitations, such as an inability to distinguish C/T SNPs from methylation calls, poor resolution of structural variants and an inability to detect specific modifications like 5-hydroxy-methylcytosine. The advent of long-read sequencing offers a powerful alternative by directly sequencing native DNA to overcome these limitations. Long-read sequencing enables the accurate detection of DNA methylation and other epigenetic marks, facilitates haplotype phasing for allele-specific studies, and resolves complex structural variation. Although challenges such as computational demands and elevated costs remain, rapid advancements in sequencing technologies, algorithmic efficiency, and declining costs are improving its accessibility. This perspective highlights the transformative potential of long-read sequencing on the study of epigenetics and genome evolution, offering a powerful tool to address critical questions in ecology and evolution.